Occurrences of Pathogens

Some microorganisms, including bacteria, viruses, and fungi, can cause human diseases. Although humans and animals are the primary reservoirs for these pathogens, some pathogens can survive and grow outside their host (e.g., soils, sediments). 

Traditionally, fecal indicator bacteria (FIB) such as E. coli have been used to predict pathogen occurrence, due to analytical obstacles to detecting and quantifying multiple pathogens in a timely manner. However, FIB of non-fecal origin are now widely recognized, and poor correlations have been reported between concentrations of FIB and pathogens. Thus, FIB may be an inadequate surrogate for predicting the occurrence of pathogens. A more reliable FIB-independent approach is needed to assess human health risks due to pathogens. 

My lab has developed a novel tool to address this issue. The tool is based on microfluidics technology and simultaneously quantifies multiple bacterial and viral pathogens. We have since applied it to monitor levels of pathogen contamination in irrigation water samples and to assess the risk of infection. Our results showed that direct multi-pathogen quantification is technically feasible for both bacterial and viral pathogens. The broader impact of these studies may be substantial: our FIB-independent direct multi-pathogen quantification approach could replace the standard, and globally ubiquitous, FIB-based approach. 

In addition, we are working to identify the sources of pathogens by sequencing the pathogen marker genes in a high throughput manner, and to clarify the ecology of pathogens, especially Arcobacter and Campylobacter, in the environments. 

Related publications:

  • Zhang, Q., J.J. Eichmiller, C. Staley, M.J. Sadowsky, and S. Ishii. 2016. Correlations between pathogen concentration and fecal indicator marker genes in beach environments. Sci. Total Environ. 573:826-830.
  • Byappanahalli, M.N., M. B. Nevers, R. L. Whitman, and S. Ishii. 2015. Application of a microfluidic quantitative polymerase chain reaction technique to monitor bacterial pathogens in beach water and complex environmental matrices. Environ. Sci. Technol. Lett. 2:347–351. 
  • Ishii, S., G. Kitamura, T. Segawa, A. Kobayashi, T. Miura, D. Sano, and S. Okabe. 2014. Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples. Appl. Environ. Microbiol. 80: 7505–7511. (Microbe magazine)
  • Ishii, S., T. Nakamura, S. Ozawa, A. Kobayashi, D. Sano, and S. Okabe. 2014. Water quality monitoring and risk assessment by simultaneous multipathogen quantification. Environ. Sci. Technol. 48:4744-4749. (Chemical and Engineering News)
  • Ishii, S., T. Segawa, and S. Okabe. 2013. Simultaneous quantification of multiple food and waterborne pathogens by use of microfluidic quantitative PCR. Appl. Environ. Microbiol. 79:2891-2898. (AEM Spotlights)